One option for the main antagonist could be a secret organization that has infiltrated Konoha. They target the Anbu prodigy because they fear the prodigy's abilities could expose their existence and plans. This organization might have members with unique and dangerous abilities themselves. They would constantly send assassins after the prodigy and try to create chaos in Konoha to keep the Anbu and the prodigy distracted while they carry out their real objectives.
The obvious main character would be the neglected Anbu prodigy. He could be someone with a tragic past that led him to the Anbu in the first place. Another important character could be Naruto himself. Even though it's about the neglected prodigy, Naruto's presence is what causes the neglect, so he would play a significant role in the story.
The Akatsuki could still be the main antagonists. Since Naruto now has Uchiha powers, they might be even more interested in him. They could see him as a threat or a valuable asset to their plans, just like they did with Sasuke.
There could be a group of ninjas who are in cahoots to keep Naruto in the shadows. They might see him as a threat to the current power structure in the village. They spread false rumors about him, or try to sabotage his training in subtle ways so that he remains an ignored prodigy. This group could be made up of some self - serving individuals who are only interested in their own status and power.
It could be an evil shinobi who wants to capture the Kitsune Anbu for their unique powers. Maybe they want to use those powers to take over the Hidden Leaf Village. Another option is a rogue Anbu member who has turned against the village and sees the Kitsune Anbu as a threat to their own plans.
It could be a rogue ANBU member who has gone bad and is trying to expose Naruto's secret identity for some evil purpose.
There's also a chance that the main character could be a completely new character from a minor clan in the Naruto universe. This character could have some hidden bloodline limit that makes them a prodigy in the ANBU. They might start as an underdog but quickly rise through the ranks due to their exceptional skills and intelligence.
Maybe an entire rival village decides to target the prodigy. They see the potential threat that the prodigy poses to their own village's dominance, so they send their best ninjas to take the prodigy down.
Perhaps a powerful shinobi from another village who has a special grudge against the Leaf's ANBU. He targets Kakashi and Naruto specifically because of their reputation within the ANBU. He has unique abilities that pose a great challenge to them, like the ability to nullify ninjutsu for short periods.
The main antagonist could be an old - school ninja who believes in the traditional and often harsh ways of the ANBU. They see Naruto's actions as weakening the village and set out to oppose him at every turn, trying to bring back the old ANBU regime.
One potential main antagonist could be an older, power - hungry shinobi who has infiltrated the Anbu in the past. This shinobi could be jealous of Naruto's sudden rise in the Anbu (due to his future knowledge) and sees him as a threat. He then starts to plot against Naruto and the Anbu's new - found positive direction. Or perhaps it's a corrupt politician in the village who uses the Anbu as a tool and doesn't want Naruto to change the Anbu's loyalty from him to the village as a whole.